Broken Roots
by Akatsuki King
Summary: Naruto is on the run for the assassination of Danzo, his former captain commander. Utilizing the sharingan he cut out of the bastard's head, one that once belonged his late friend Shisui, Naruto seeks to cut away the rot that threatens to destroy Konoha. Dark/Smart Naruto. Assassin Naruto. Vote for pairings.


**Author's Notes** : Inspiration is a nasty bitch. I've been wanting to write something like this for a while now, finally sat down and typed it out. Forgive the rough format, and any spelling or grammar mistakes you find. I don't have a beta, and I wanted to post this so badly I barely proof read it.

Combined with _The Salad in my Ramen_ this is two new stories in one week. I'm on a role! I plan to update both relatively frequently, and have already finished the first half of _The Salad in my Ramen's_ next chapter. Anyways, on to the story.

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Disclaimer: I do not own Naruto.

Email: Just PM me.

 _Italicized_ – for a person's internal monologue/thoughts, and emphasis.

 **Bold** – for Author's Notes. You should read them, you impatient bastard.

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Chapter 1

Soft murmurs permeated the night air. The barely audible rustles of cloth, or swish of a cloak were the only sign that ninjas were on the move. Dozens of jonin and Anbu flooded the village; long, dark silhouettes that moved across the rooftops like shadows.

 _They're good._ Naruto thought absently. Hidden beneath his Meisaigakure (hiding with camouflage) no jutsu, he appeared as little more than a distortion in the air. His proficiency with the technique allowed for his scent and chakra signature to be completely concealed to all but the most talented trackers.

Unfortunately for him, Konoha had quite a few top notch trackers.

 _One, two, three…_ Naruto counted off the chakra signatures moving his way.

 _Five._ Either these Anbu were very skilled sensors, or Hyuugas.

The outer wall of the village loomed in the distance. They no doubt assumed this to be his destination. Naruto banked left, heading in the opposite direction, deeper into the village.

His superior speed and agility allowed Naruto continually outmaneuver the Anbu on his tail, if only for the time-being.

One slip up, one wrong step, and he'd be done for.

Naruto knew he had to time this right to succeed. He had thrown all of himself into planning tonight. Months had been spent strategizing, information gathering, and training to ensure the success of his mission.

The assassination of Danzo.

His former captain commander.

The Anbu on his back were closing in. By now, Naruto had identified two as Hyuuga, due to the unique way they molded their chakra to perform the shunshin technique. His nose told him that other two were Inuzaki, and the last chakra signature he recognized even though it was extremely well hidden.

Yamanaka Inoichi, one of his old senseis. It was only due to Naruto's familiarity with the man's chakra that Naruto was able to identify him at all. A terrifyingly intelligent shinobi, and undoubted the best sensor in the entire village, Inoichi was one of Konoha's few high jonin.

Not a man to be taken lightly.

 _But neither am I_. Naruto mused.

An accomplished shinobi by the age of eight, Naruto had been pulled from the regular ninja forces and placed in Anbu. During his short, 8 month stint in the division, he'd trained with a number of experienced shinobi and squad leaders. Inoichi was one of them. Nearly everything Naruto knew about sensory techniques he'd learned from the Yamanaka.

But Naruto's talent drew too much attention, and it wasn't long before he was drafted into a special branch of Anbu known as 'Root'. He was in the program for eleven months before being promoted to the rank of jonin. He was ten at the time. It was only a month later that the Hokage officially disbanded the division.

That was year ago.

Naruto shook his head to clear his thoughts. He had no time to get lost in memories now, not with five jonin on his tail.

 _If Inoichi gets much closer I'll be within range of his mindreading technique. He may be able to read my surface thoughts and figure out my plan._

Naruto dropped his Meisaigakure no jutsu as he finished making the final preparations for his escape. Stealth all but abandoned, Naruto poured chakra into his legs. Shunshin after shunshin, he drew ever closer to his destination.

Daisan Enshujo, although most ninja referred to it as training ground 3, was a portion of land located inside of Konoha. A river ran through it, and dense forest rose on the both of its sides. At its center sat a glade, with three tree stumps set up in a triangular position.

It was here that Naruto had painstakingly planned his escape.

Naruto came to a stop in the middle of the glade, right in the center of the three stumps.

His right hand already bleeding from a self-inflicted kunai wound, Naruto wiped his blond onto the top of the nearest stump before launching into a stream of handseals.

He didn't pause as the five ninja trailing him landed in a circle, surrounding him.

"Halt! You are under arrest for the assassination of Fu Yamanaka, Aburame Torune, and council member Danzo Shimura!" It was one of the Hyuuga that spoke, a raven haired man with a bear mask on. Naruto idly noted that the second Hyuuga was none other than clan head Hyuuga Hiashi.

"Naruto, what-?" Inoichi's breath hitched in his throat as his eyes locked with Naruto's. One incandescent blue, and the other crimson red with three black tomo. The tomo in Naruto's eye blended together in one fluid movement, forming a black four-pronged star shape.

Naruto felt the mind-reader delve into his head, looking for answers.

 _It once belonged to Shisui-nisan, until Danzo cut it out of his head and stole it for himself._

Naruto thought at Inoichi, not sure how his friend and former sensei would react to the information.

 _I took it back._

Like a damn breaking, a flood of information poured out of Naruto's head. He hoped it would stall the Yamanaka long enough for him to finish his jutsu.

Inoichi took a step back, overcome by the onslaught of data. Ramen recipes, shuriken throwing techniques, various katas, the entire bingo book… an endless stream of random thoughts flowed into Inoichi's head faster than he could process it. Naruto was no doubt using the senseless information to mask his true intentions. Mentally shoving the thoughts aside, and filing them away for later examination, Inoichi returned to raking his way through Naruto's mind.

 _You're too late Ichi-sama. I'm sorry._

The mind-reader's eyes grew wide as he realized exactly what he was looking at.

Nicknamed a 'jump-spot' by Anbu, its official name was the Jikukan Ido (Time-Space Migration) no Jutsu. It was an A-class ninjutsu used to teleport people or objects across space and time between two preset points. It was a rarely used technique, mostly due to the large amount of time involved in preparation. But once completed, it could be utilized to teleport the user between two preset destinations instantaneously.

So long as you knew the specific hand-sign sequence formulated to activate it.

"Hiashi, he's preparing a Jikukan (time-space) ninjutsu!" Inoichi shouted.

Before Inoichi could finish his sentence, Hiashi moved to attack. In an act of pure speed the man disappeared, blurring back into existence directly behind Naruto. A single palm shot forward, cloaked in debilitating white chakra.

Just as Naruto's hands formed the ram seal. The three tree stumps surrounding him lit up with intricately carved seals, and in a single flash of brilliant blue light, Naruto was gone.

Hiashi's attack landed a moment too late, sailing through now empty air.

"Shit!" The normally calm and calculated Inoichi yelled.

"It will take us days to crack the sequence he created to activate his Ido technique! He'll have destroyed the other location by then. Useless!" Inoichi threw his arms up in the air and stomped a few feet away. He needed calm down and sift through the information Naruto poured at him. If he knew Naruto half as well as he thought he did, the reason for all this was buried somewhere inside those memories and jumbled up thoughts.

"Bear!"

"Yes sir!"

"Report Naruto's escape to the Hokage. Crow, get Kakashi here NOW and send word to Jiraiya. We need them to start decoding the Jikukan Ido's seal as soon as possible. Even if it won't take us to him, it might tell us where he went."

"Hai!" The two Anbu said in unison before they poofed away.

 _Why Naruto?_ If what Naruto said was true, if Danzo really had cut that eye out of Shisui…

 _You should have come to me. You should have trusted me._

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Giant, moss covered trees grew from the murky, ankle-deep water. Beautiful flowering plants hung from their colossal branches, splashes of color against a mostly green and brown canvas. Even though the flower-petals were beginning to wilt and die, their bright colors remained. The moon was full tonight; its silvery glow gave the swamp an almost ethereal look.

It was actually kind of beautiful.

For a swamp at least.

Right in the center of it all stood three stone pillars, spaced out in a triangular formation. Crumbled with age, their grey forms only stood a few feet above the water. Blue, runic symbols webbed across their surface, and a flash lit up the night.

A blond child appeared in the center of the stone formation. The boy fell to his knees with a splash, panting in exhaustion.

Shoulder length blonde hair fell about his face, the golden strands casting his features into shadow. Two mismatch eyes peered out from the darkness, one red, one blue. A dark smirk tugged on his lips, looking out of place on his eleven year old face.

Naruto straightened, appraising his surroundings. He was in swamp country. More specifically, he was just south of Okamiyata, swamp country's capital. A small, non-militarized city with virtually no ninja populace, Okamiyata was a perfect place for Naruto to hideout for the time being.

A sudden gust stirred the swamp's chilled air. It stung at the bare skin of Naruto's unprotected face. The blond pulled his flak jacket tighter around his body in the hopes of stopping the unexpected shivers that ran down his spine. It was unusually cold for October, or at least it was compared to Konoha. Swamp country had a shorter summer than the Hidden leaf, and winter was already blooming in the peripheral edges of the fall.

 _There's no going back now._ With that final thought in his mind, Naruto took off in the direction of Okamiyata.

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The wind's harsh chill bit into the man's exposed flesh, yet he did not seem to notice. A half-empty glass bottle hung loosely in his left hand, and the saccharine stench of alcohol hung about him.

The drunk staggered down the side of an old, weathered road. Brittle, dead grass crunched beneath his worn leather shoes. He was not quite sure where he was going. It was as if his body was acting of its own accord.

Tripping he stumbled onto his hands and knees panting. His chest felt heavy, as if a snake was constricting around his torso. Gasping for air, he rolled onto his back, watery eyes gazing up at the murky, moonlit sky.

The constricting feeling died slowly, replaced with an atypical feeling of numbness and warmth. It was a sensation only alcohol could give, a sense a closure that helped him to forget his past, his mistakes. A smile graced his lips, a scarce occurrence in the latter-days of his life. It wouldn't last long.

A drop of something cold and wet landed on the bridge of his nose. It was followed by another, and another. The drops grew in number, until he was being pelted by ice-cold rain. It was as if God was trying to wake him from his bliss-filled intoxication. Grunting, he pulled his body into an awkward sitting position. He stayed there for who knows how long, just soaking in the rain.

Finally, he shook himself to his feet. The buzz of alcohol had died down enough for him to recognize the area. The red light district of south Okamiyata. He patted his right pocket to make sure wallet was still there. It was. The man grinned broadly. He had been paid earlier that morning, so he had money to blow.

 _I'll have me a woman tonight_. He thought drunkenly. Realizing he had dropped his drink, he fumbled around in the dark for a few moments, until his hands closed around its slick surface.

After several tries, his numbed fingers were able to tug the cap off, and he took a long hard swig, letting the alcohol smolder its way down his throat. Starting off again, it was only a few minutes until he found where he wanted to be. It was a dirty looking building on a little side street. The large wooden sign read _Twisted Knickers._

His grin grew wider and he strode in.

"Whatcha want tonight Akio?" A tall, sickly looking man asked from behind a counter.

"Just send up one of the pretty ones. You know what I like." The man, now identified as Akio, said lecherously.

The sickly man nodded and handed Akio a key before waving him on. The key had the number _113_ engraved on it.

 _Sweet, first floor._ Akio thought to himself. It was probably for the best considering how drunk he was that he didn't have to tackle stairs. He stopped in front of his door and fumbled with the keys.

"Fuckin pain…" He grumbled before finally managing to work the lock. The door swung open, revealing a tiny little room. Stained wall paper that had once been white, but was now more of a yellow green clung to the walls, peeled off in places. A box TV sat on a small stand at the foot of a twin sized bed. To his left was a crusty looking door that led to an equally shitty looking bathroom.

But Akio didn't mind the state of the room. He came he for the company.

Raising the bottle to his lips Akio shot-gunned the rest of the vodka before flinging the empty bottle at small trash-bin in the corner. It missed by a lot, shattering against the white/yellow/green wall. Akio stumbled in, kicked the door shut behind him and fell back-first onto the bed.

It took Akio's numb fingers several seconds to get his belt undone, and several more get it off. Tossing it aside with a satisfied grunt, he began to work on removing his pants. He had them about halfway off when he felt it. The hairs rose on the back of his neck, and his heart skipped a beat.

Someone was in the room with him. And considering he couldn't see, hear, or sense anything, it had to be a rather special kind of ninja.

Akio tried and failed to pull himself out of his drunken stupor, but it was too late. He blinked, and in that second the sharp point of a kunai appeared in front of his left eye.

"Shit shit shit!" he exclaimed. "What do you want? I'm not a ninja any more, I don't do that shit!"

Even though the blade blocked the eyesight of his left eye, he could see the assassin out of his right. A small looking, black clad ninja was crouched on top of him. One arm held Akio down, and the other held the kunai over his eye.

Akio looked into the face of the shinobi and was surprised to see a child looking back at him. Both cheeks were tattooed with black, whisker-like marks. A halo of blond hair fell around the kid's face. A mismatched pair eyes gazed down out him; one incandescent blue, the other the blood red of a sharingan.

"Oh fuck me, fuck me! What do you want?" Akio whimpered. He was dead. He knew it.

"Information... on Danzo."

Akio's eyes widened in fear. This was about Danzo? Shit! Why did he have to get involved with that man? He knew it would get him into trouble.

"I-I'm sorry! Bu-but I can't tell you anything! Pah-plea-" Akio's sentence was cut short as the boy's free hand moved to his throat and squeezed.

"Danzo is dead. His seal is now void so you can speak freely." The assassin tightened his grip. Akio knew his throat would collapse if the boy so much as twitched.

"Tell me or die."

The boy eased up on his grip. Akio coughed and gasp for breath.

 _Danzo dead?_ _Impossible!_ Such a young boy had no chance of killing that man. Still, if what this ninja said was true...

He was dead if he didn't cooperate anyways.

"Please don't kill me! I'm just an informant! If Danzo's really dead, I'll tell you everything!"

Naruto smirked as the large man squirmed in his grasp. Danzo should have picked his informants more wisely. This pathetic man, Akio Mashirama, may have once been a shinobi, but there was a reason he retired so early. The man was a lousy piece of shit, a rapist and a coward.

 _That old man had too much faith his despicable cursed seal._ Naruto was referring to Danzo's Zekka Konzetsu no Jutsu, or Cursed Tongue Eradication Technique. It caused the wearer's entire body to freeze up if they tried to reveal any incriminating information about Danzo or Root. This rendered the wearer unable to speak or move during an interrogation. Naruto had checked his tongue the first chance he got to make sure those three solid lines and two broken ones were no longer tattooed onto the back of his tongue. With Danzo dead, the seal disappeared and was now useless.

The three tomo of Naruto's sharingan eye spun madly as he cast a genjutsu on the man. He wanted to… _encourage_ honesty. This information had to be accurate.

"Start from the beginning."

 **Author's Notes** : Good? Bad? Ugly? Wonderful? What do you think? Just like my other new story, _The Salad in my Ramen_ , I'm looking for as much feedback as possible. Plot holes, ideas, encouragement or criticism, let me know! I welcome all forms of critique, and the more feedback I get the sooner I can get started on the next chapter.

Reviews of any length and or type are welcome (long and short, criticism or critique). Don't forget to vote for pairings, assuming you have a preference. No yoai please.


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